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- PDB-4izz: Crystal Structure of Fischerella Transcription Factor HetR comple... -

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Basic information

Entry
Database: PDB / ID: 4izz
TitleCrystal Structure of Fischerella Transcription Factor HetR complexed with 21mer DNA target
Components
  • DNA (5'-D(*GP*TP*GP*AP*GP*GP*GP*GP*TP*TP*AP*AP*AP*CP*CP*CP*CP*TP*CP*AP*C)-3')
  • Transcription Factor HetR
KeywordsTranscription/DNA / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / helix-turn-helix / DNA-binding domain / transcription factor / Transcription-DNA complex
Function / homology
Function and homology information


heterocyst development / serine-type endopeptidase activity / proteolysis / DNA binding
Similarity search - Function
HetR, flap domain / HetR, N-terminal DNA-binding domain / Peptidase S48, DNA-binding transcriptional activator HetR / HetR, C-terminal Hood domain / HetR, flap domain / HetR, N-terminal DNA-binding domain / Peptidase family S48 / Heterocyst differentiation regulator C-terminal Hood domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Heterocyst differentiation protein
Similarity search - Component
Biological speciesFischerella thermalis (bacteria)
Anabaena (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsKim, Y. / Joachimiak, G. / Gornicki, P. / Joachimiak, A. / MCSG / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structures of complexes comprised of Fischerella transcription factor HetR with Anabaena DNA targets.
Authors: Kim, Y. / Ye, Z. / Joachimiak, G. / Videau, P. / Young, J. / Hurd, K. / Callahan, S.M. / Gornicki, P. / Zhao, J. / Haselkorn, R. / Joachimiak, A.
History
DepositionJan 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Jun 5, 2013Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription Factor HetR
B: Transcription Factor HetR
C: DNA (5'-D(*GP*TP*GP*AP*GP*GP*GP*GP*TP*TP*AP*AP*AP*CP*CP*CP*CP*TP*CP*AP*C)-3')
D: DNA (5'-D(*GP*TP*GP*AP*GP*GP*GP*GP*TP*TP*AP*AP*AP*CP*CP*CP*CP*TP*CP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7769
Polymers83,3634
Non-polymers4125
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20190 Å2
ΔGint-193 kcal/mol
Surface area32770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.425, 92.425, 96.366
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
DetailsAs in the asymmetric unit

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Components

#1: Protein Transcription Factor HetR


Mass: 35233.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella thermalis (bacteria) / Strain: PCC 7521 / Gene: hetR / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q2ACK9*PLUS
#2: DNA chain DNA (5'-D(*GP*TP*GP*AP*GP*GP*GP*GP*TP*TP*AP*AP*AP*CP*CP*CP*CP*TP*CP*AP*C)-3')


Mass: 6448.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: the DNA sequence occurs in Anabaena / Source: (synth.) Anabaena (bacteria)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 24 % Polyvinylpyrrolidone, 50 mM Hepes pH 8.0, 100 mM sodium chloride, 10 mM magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 31681 / Num. obs: 31681 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 58.8 Å2 / Rsym value: 0.057 / Net I/σ(I): 15.4
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 1563 / Rsym value: 0.744 / % possible all: 99.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QOD

3qod


Resolution: 2.502→30.786 Å / SU ML: 0.32 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1595 5.04 %random
Rwork0.182 ---
all0.185 31655 --
obs0.185 31655 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.5 Å2
Refinement stepCycle: LAST / Resolution: 2.502→30.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4828 856 23 159 5866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035996
X-RAY DIFFRACTIONf_angle_d0.6868282
X-RAY DIFFRACTIONf_dihedral_angle_d17.1982367
X-RAY DIFFRACTIONf_chiral_restr0.046881
X-RAY DIFFRACTIONf_plane_restr0.003921
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.502-2.58270.32711520.26682707285999
2.5827-2.67490.26511340.245727382872100
2.6749-2.7820.2581410.233727692910100
2.782-2.90850.33251320.238227362868100
2.9085-3.06170.30971410.228427502891100
3.0617-3.25330.2781430.230527202853100
3.2533-3.50420.24541420.200327732915100
3.5042-3.85620.20271440.175227322875100
3.8562-4.41280.18881580.153326992857100
4.4128-5.55440.19481700.148427242894100
5.5544-30.78870.20331380.16292712285098
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9307-0.01321.14992.4122-0.44752.3970.04450.16240.1139-0.0322-0.0313-0.21020.260.24040.00310.47760.02690.06830.3798-0.04480.369248.1368-3.7946-1.1082
22.209-0.92790.2314.4466-1.6234.14190.04480.0184-0.093-0.25540.17160.24380.0333-0.2177-0.2110.5002-0.08060.10090.3586-0.04520.416928.8654-1.4276-28.5299
32.6234-0.0685-0.24822.7842-0.47162.26810.16540.05680.01960.0004-0.4033-0.0419-0.04640.0340.23180.4081-0.0561-0.1140.42430.03050.412846.59724.5025-2.2138
42.1052-0.71591.13292.6202-0.29484.43440.12120.18850.4486-0.15820.0611-0.59550.35310.471-0.16690.41090.01940.09060.4525-0.03410.525652.07722.4815-0.7204
52.4665-0.30190.77511.91590.86591.9102-0.0052-0.4315-0.04750.2099-0.16160.19570.2763-0.58040.16780.4806-0.06010.08070.4125-0.01780.371829.1155-4.56641.4948
61.2733-0.3352-0.18962.32760.21453.30140.2926-0.138-0.51840.36140.17990.1270.0494-0.4393-0.24650.50760.068-0.00030.40830.14480.494652.42970.354932.919
74.2254-0.1962-1.56945.3471-3.53255.9559-0.0595-0.25070.28210.3677-0.3485-0.944-0.23080.6848-0.02430.64990.0839-0.07650.66930.04610.684869.758-4.019140.0931
81.64120.77830.81952.97661.11223.92140.20570.0435-0.12730.304-0.14190.23220.6204-0.4808-0.03910.52110.02880.01610.35860.0790.476750.0212-7.841124.1742
91.6635-1.28553.23561.0972-2.27824.24790.19270.1493-0.4836-0.08030.11270.35130.14460.2234-0.2580.46560.0539-0.06850.428-0.02610.490852.64846.057916.2242
103.87240.5833-0.32272.4074-0.42411.9580.0683-0.42120.3802-0.0048-0.22810.2035-0.13030.22820.17680.4594-0.0654-0.12460.4102-0.00370.388546.889728.6110.1306
112.4354-1.00240.46071.76071.10981.3660.2805-0.1859-0.64430.40740.11740.7283-0.02580.0717-0.25870.7028-0.17930.06170.75170.02430.739916.3881-15.3886-9.1429
124.51430.40421.66677.6810.3126.3131-0.8520.0545-0.00060.2381.15560.0101-0.2387-0.2726-0.46560.8738-0.0737-0.07370.52740.02420.615931.3473-26.0966-6.9483
133.74080.18722.20663.3618-0.98397.63720.42460.2641-0.85960.13941.1031-0.08710.0430.2066-1.43870.7962-0.0376-0.07920.50210.0450.675745.7685-18.38673.5049
149.7412-0.2896-1.57491.1382-0.31310.9041-1.5648-0.2201-1.84960.12010.2703-0.54230.59871.50580.86191.29140.3853-0.03161.11920.05171.488559.7111-27.808413.8753
152.3156-1.4911-1.70861.04090.47636.1145-1.29510.2165-1.5274-0.04930.319-0.50531.09591.45261.05951.43890.3676-0.03641.5259-0.26851.973472.8317-25.242311.9054
163.27320.463-1.0152.1141-1.53761.2554-0.134-0.1156-0.50290.1956-0.0263-0.4518-0.1311-1.19250.20650.91330.2612-0.09630.8593-0.17361.06964.2517-20.93029.1359
173.3368-1.34771.81862.44390.19923.5453-0.34410.1831-1.05170.17341.446-0.15360.19040.8284-0.34881.05330.1614-0.05640.6162-0.12670.998747.176-27.82086.6135
183.9534-0.1638-0.15672.08551.32741.1915-0.1708-0.1483-0.70470.26980.25390.18240.2201-0.504-0.17020.6353-0.08220.03450.52880.09760.640225.3513-19.7186-9.0084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 100 )
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 220 )
3X-RAY DIFFRACTION3chain 'A' and (resid 221 through 298 )
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 34 )
5X-RAY DIFFRACTION5chain 'B' and (resid 35 through 100 )
6X-RAY DIFFRACTION6chain 'B' and (resid 101 through 123 )
7X-RAY DIFFRACTION7chain 'B' and (resid 124 through 139 )
8X-RAY DIFFRACTION8chain 'B' and (resid 140 through 192 )
9X-RAY DIFFRACTION9chain 'B' and (resid 193 through 242 )
10X-RAY DIFFRACTION10chain 'B' and (resid 243 through 298 )
11X-RAY DIFFRACTION11chain 'C' and (resid -10 through -6 )
12X-RAY DIFFRACTION12chain 'C' and (resid -5 through -1 )
13X-RAY DIFFRACTION13chain 'C' and (resid 0 through 4 )
14X-RAY DIFFRACTION14chain 'C' and (resid 5 through 9 )
15X-RAY DIFFRACTION15chain 'C' and (resid 10 through 10 )
16X-RAY DIFFRACTION16chain 'D' and (resid -10 through -6 )
17X-RAY DIFFRACTION17chain 'D' and (resid -5 through -1 )
18X-RAY DIFFRACTION18chain 'D' and (resid 0 through 10 )

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